Re: [ccp4bb] Trouble with conversion from HKL to CCP4 file format
Hi, I added some explanation for the XSCALE output to the XDSwiki at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv#explanation_of_typical_output . hope this helps, Kay
Re: [ccp4bb] difference between polar angle and eulerian angle
The polar angles ϕ, ω define the direction of an axis about which a rotation by angle κ occurs, i.e. a single rotation around a defined axis. This is different from Eulerian angles which define 3 successive rotations around principal axes On 27 Mar 2014, at 06:11, Qixu Cai wrote: > Dear all, > > From the definition of CCP4 > (http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle (ϕ, ω, κ) > can be visualised as rotation ϕ about Z, rotation ω about the new Y, rotation > κ about the new Z. It seems the same as the ZXZ convention of eulerian angle > definition. What's the difference between the CCP4 polar angle definition and > eulerian angle ZXZ definition? > > And what's the definition of polar angle XYK convention in GLRF program? > > Thank you very much! > > Best wishes, > > -- > Qixu Cai > Email: caiq...@gmail.com > School of Life Sciences, > Xiamen University, Fujian, China > **from thunderbird**
[ccp4bb] maltose binding protein
Dear CCP4 Does anyone know how to remove the maltose binding protein after cleavage from the target protein; I have tried gel filtration and ion exchange but with no luck, my protein is interacting with the MBP even after complete cleavage. I would be grateful for any help or suggestions Best Regards Rana
Re: [ccp4bb] maltose binding protein
Dear Mark Thank you for yor reply, and yes I have tried adding it to the maltose resin after cleavage but the MBP runs through with my protein, I have also tried 1M NaCl but with no luck and I also apply detergent after cleavage to the dialysis buffer because I usually dialyze after cleavage , is there anything that could maybe precipitate the MBP Best Regards Rana From: Mark J van Raaij To: rana ibd Sent: Thursday, March 27, 2014 11:35 AM Subject: Re: [ccp4bb] maltose binding protein did you try the maltose-resin? in principle it should bind MPB but not your protein. You can try to add salt or detergents to disturb interaction between MBP and your protein (also in gel filtration). No guarantee of success, unfortunately not all protein behave "nicely". Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Mar 2014, at 11:26, rana ibd wrote: > Dear CCP4 > Does anyone know how to remove the maltose binding protein after cleavage > from the target protein; I have tried gel filtration and ion exchange but > with no luck, my protein is interacting with the MBP even after complete > cleavage. I would be grateful for any help or suggestions > Best Regards > Rana
[ccp4bb] symmetry related water
Dear All, I have newly obtained pdb model for my protein where the waters are not numbered according to the chain they belong to. I generated symmetry related molecules for some chains but the waters are together. I would appreciate suggesstions if there is a way out to get symmetry related water specific for a chain type without manually editing the pdb by visual inspection? Thank you in advance. Urvashi
Re: [ccp4bb] difference between polar angle and eulerian angle
This is a helpful introductory paper on the topic: http://journals.iucr.org/d/issues/2001/10/00/ba5006/ba5006.pdf -- David On 27 March 2014 06:11, Qixu Cai wrote: > Dear all, > > From the definition of CCP4 (http://www.ccp4.ac.uk/html/ > rotationmatrices.html), the polar angle (ϕ, ω, κ) can be visualised as > rotation ϕ about Z, rotation ω about the new Y, rotation κ about the new Z. > It seems the same as the ZXZ convention of eulerian angle definition. > What's the difference between the CCP4 polar angle definition and eulerian > angle ZXZ definition? > > And what's the definition of polar angle XYK convention in GLRF program? > > Thank you very much! > > Best wishes, > > -- > Qixu Cai > Email: caiq...@gmail.com > School of Life Sciences, > Xiamen University, Fujian, China > **from thunderbird** >
Re: [ccp4bb] difference between polar angle and eulerian angle
The figures 4 and 5 in Chapter 11 BMC also help to visualize the difference http://www.ruppweb.org/garland/gallery/Ch11/pages/Biomolecular_Crystallography_Fig_11-04_PART2.htm http://www.ruppweb.org/garland/gallery/Ch11/pages/Biomolecular_Crystallography_Fig_11-05.htm Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans Sent: Donnerstag, 27. März 2014 11:11 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] difference between polar angle and eulerian angle The polar angles ?, ? define the direction of an axis about which a rotation by angle ? occurs, i.e. a single rotation around a defined axis. This is different from Eulerian angles which define 3 successive rotations around principal axes On 27 Mar 2014, at 06:11, Qixu Cai wrote: > Dear all, > > From the definition of CCP4 > (http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle (?, ?, ?) > can be visualised as rotation ? about Z, rotation ? about the new Y, rotation > ? about the new Z. It seems the same as the ZXZ convention of eulerian angle > definition. What's the difference between the CCP4 polar angle definition and > eulerian angle ZXZ definition? > > And what's the definition of polar angle XYK convention in GLRF program? > > Thank you very much! > > Best wishes, > > -- > Qixu Cai > Email: caiq...@gmail.com > School of Life Sciences, > Xiamen University, Fujian, China > **from thunderbird**
Re: [ccp4bb] difference between polar angle and eulerian angle
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, maybe the confusion is due to that your quote seems incomplete. According to the html-side the 'visualisation' includes two back-rotations in addition to what you copied here, so there is at least one difference to the visualisation of the Eulerian angles. Best, Tim On 03/27/2014 07:11 AM, Qixu Cai wrote: > Dear all, > > From the definition of CCP4 > (http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle > (ϕ, ω, κ) can be visualised as rotation ϕ about Z, rotation ω about > the new Y, rotation κ about the new Z. It seems the same as the ZXZ > convention of eulerian angle definition. What's the difference > between the CCP4 polar angle definition and eulerian angle ZXZ > definition? > > And what's the definition of polar angle XYK convention in GLRF > program? > > Thank you very much! > > Best wishes, > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTNAz0UxlJ7aRr7hoRAj7IAKDs/J0L/XCYPpQSyB2BPJ2uWV2lVgCeKD72 0DemwU57v6fekF6iOC4/5IA= =PeT9 -END PGP SIGNATURE-
[ccp4bb] Thank you
Dear CCP4 Thank you for all your suggestions Best Regards Rana
[ccp4bb] sorry, sort of off topic
I'm after suggestions as to where the best place(s) for obtaining info on latest equipment - advances in techniques etc. Oh, for protein crystallisation and screening ahead of data collection! cheers Dean
Re: [ccp4bb] maltose binding protein
Dear Rana, Did your protein come out from the void volume of gel filtration column? In my case, I have expressed a soluble aggregated protein which always like to interact with MBP. Kind regards, Wenhe > On 27 Mar, 2014, at 6:26 pm, rana ibd wrote: > > Dear CCP4 > Does anyone know how to remove the maltose binding protein after cleavage > from the target protein; I have tried gel filtration and ion exchange but > with no luck, my protein is interacting with the MBP even after complete > cleavage. I would be grateful for any help or suggestions > Best Regards > Rana
Re: [ccp4bb] maltose binding protein
Rana, It is hard to answer you question without more details (MW and pI of your target protein). MBP binds very well to amylose resins and is usually quite easily bound to anion exchange resins. Did you just run a "standard" ion exchange protocol or try different pH regimes? However, you did mention you have used a detergent. Why do you do that? MBP binding to amylose resins can be markedly disturbed in the presence of several different detergents, which is a particularly bad thing for a membrane protein fusion. That is why all our MBP fusion constructs have an additional His-tag. If you really don't need the detergent, leave it out, then try the amylose resin again. One other point is how old is your amylose resin and, if you express in E. coli, do you regularly add a little glucose to the media? Amylose resin is degraded by E. coli amylases, which I believe is suppressed when glucose is in the medium. However, inferring from your email, I would suppose that you initially purified the MBP fusion using the amylose resin. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Mar 27, 2014, at 6:49 AM, rana ibd wrote: > Dear Mark > Thank you for yor reply, and yes I have tried adding it to the maltose resin > after cleavage but the MBP runs through with my protein, I have also tried 1M > NaCl but with no luck and I also apply detergent after cleavage to the > dialysis buffer because I usually dialyze after cleavage , is there anything > that could maybe precipitate the MBP > Best Regards > Rana > > > From: Mark J van Raaij > To: rana ibd > Sent: Thursday, March 27, 2014 11:35 AM > Subject: Re: [ccp4bb] maltose binding protein > > did you try the maltose-resin? > in principle it should bind MPB but not your protein. You can try to add salt > or detergents to disturb interaction between MBP and your protein (also in > gel filtration). > No guarantee of success, unfortunately not all protein behave "nicely". > > Mark J van Raaij > Lab 20B > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > > > > > On 27 Mar 2014, at 11:26, rana ibd wrote: > > > Dear CCP4 > > Does anyone know how to remove the maltose binding protein after cleavage > > from the target protein; I have tried gel filtration and ion exchange but > > with no luck, my protein is interacting with the MBP even after complete > > cleavage. I would be grateful for any help or suggestions > > Best Regards > > Rana > >
[ccp4bb] Merging Data from Multiple Crystals
Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
[ccp4bb] Merging Data from Multiple Crystals
I am also trying to merge data from multiple crystals that I collected from. I have tried to reindex the data in CCP4 after indexing in iimosflm, and then put these .mtz files through sortmtz before scala, but I keep getting an error in sort mtz: From ccp4_lwbat: warning: attempt to add new batch with existing batch number 1! SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above Times: User: 0.3s System:0.0s Elapsed: 0:00 *** * Information from CCP4Interface script *** The program run with command: /Applications/ccp4-6.4.0/bin/sortmtz HKLOUT "/Users/bruner/Desktop/combinedfiles.mtz" has failed with error message SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above *** #CCP4I TERMINATION STATUS 0 " SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above" #CCP4I TERMINATION TIME 26 Mar 2014 18:50:58 #CCP4I MESSAGE Task failed Any help would be greatly appreciated!
[ccp4bb] cTruncate problem
I can index my data through imosflm with no problems, but when I try to scale using aimless, the program will not run if I also run truncate (or old truncate). Here is the error message I get below. Could anyone elaborate on what this means? Thanks. P.S. I can take the scaled .mtz file from aimless that was not truncated and get an ok MR solution. COMPLETENESS ANALYSIS (using intensities): Using I/sigI > 3 with completeness above 0.85, the estimated useful Resolution Range of this data is 17.964A to 8.982A The high resolution cut-off will be used in gathering the statistics for the dataset, however the full dataset will be output TRANSLATIONAL NCS: No translational NCS detected (with resolution limited to 8.98 A) ANISOTROPY ANALYSIS (using intensities): Eigenvalues: 0. 0. 0. Eigenvalue ratios: nan nan nan ctruncate: Anisotropy correction failed - negative eigenvalue. Times: User: 0.5s System:0.0s Elapsed: 0:00 *** * Information from CCP4Interface script *** The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate -hklin "/tmp/bruner/ClbM_29_3_mtz.tmp" -hklout "/tmp/bruner/ClbM_29_5_mtz_New.tmp" -colin "/*/*/\[IMEAN,SIGIMEAN\]" -colano "/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\]" -colout New has failed with error message ctruncate: Anisotropy correction failed - negative eigenvalue. ObjectCache: Leaked 0005 refs to *** #CCP4I TERMINATION STATUS 0 " ctruncate: Anisotropy correction failed - negative eigenvalue. ObjectCache: Leaked 0005 refs to " #CCP4I TERMINATION TIME 25 Mar 2014 18:32:11 #CCP4I TERMINATION OUTPUT_FILES /tmp/bruner/ClbM_29_2_mtz.tmp ClbM /Users/bruner/Desktop/Jarrod/ClbM_29.scales ClbM /Users/bruner/Desktop/Jarrod/ClbM_29_rogues.log ClbM /Users/bruner/Desktop/Jarrod/ClbM_29_normplot.xmgr ClbM /Users/bruner/Desktop/Jarrod/ClbM_29_anomplot.xmgr ClbM /Users/bruner/Desktop/Jarrod/ClbM_29_rogueplot.xmgr ClbM /Users/bruner/Desktop/Jarrod/ClbM_29_correlplot.xmgr ClbM #CCP4I MESSAGE Task failed
Re: [ccp4bb] Merging Data from Multiple Crystals
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jarrod, try pointless and aimless to merge the data, this should get rid of this error message. Otherwise you would have to renumber the batches, which might be tedious and also unnecessary since pointless has been around. Best, Tim On 03/27/2014 03:17 PM, Jarrod Mousa wrote: > I am also trying to merge data from multiple crystals that I > collected from. I have tried to reindex the data in CCP4 after > indexing in iimosflm, and then put these .mtz files through > sortmtz before scala, but I keep getting an error in sort mtz: > > From ccp4_lwbat: warning: attempt to add new batch with existing > batch number 1! SORTMTZ: LWBAT: error in ccp4_lwbat, see messages > above Times: User: 0.3s System:0.0s Elapsed: 0:00 > > > > *** > > > * Information from CCP4Interface script > *** > > > The program run with command: /Applications/ccp4-6.4.0/bin/sortmtz HKLOUT "/Users/bruner/Desktop/combinedfiles.mtz" > has failed with error message SORTMTZ: LWBAT: error in > ccp4_lwbat, see messages above > *** > > > > > #CCP4I TERMINATION STATUS 0 " SORTMTZ: LWBAT: error in > ccp4_lwbat, see messages above" #CCP4I TERMINATION TIME 26 Mar 2014 > 18:50:58 #CCP4I MESSAGE Task failed > > > Any help would be greatly appreciated! > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTNDfkUxlJ7aRr7hoRAvLSAJ0de7psQe68MoHYq1ZMPGEJTtvwGgCfTj6X tu1A/xsYbi+30ZwDbRPEO5g= =4k8U -END PGP SIGNATURE-
Re: [ccp4bb] cTruncate problem
On 27 March 2014 14:23, Jarrod Mousa wrote: > Using I/sigI > 3 with completeness above 0.85, the estimated useful > Resolution Range of this data is 17.964A to 8.982A > Hi, I would imagine that the message above has something to do with it. Cheers -- Ian
Re: [ccp4bb] Merging Data from Multiple Crystals
Hi, You may also try BLEND to choose the optimal data sets before scaling and merging Foadi J, Aller P, Alguel Y, Cameron A, Axford D, Owen RL, Armour W, Waterman DG, Iwata S & Evans G (2013) Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 69: 1617–1632 Tassos Papageorgiou Jarrod Mousa wrote: Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
Re: [ccp4bb] sorry, sort of off topic
Hi Dean: Why not check out this excellent book: Bergfors, T., Editor. Protein Crystallization: Second Edition. 2009. International University Line, La Jolla, California, 500 pp. http://xray.bmc.uu.se/terese/buybook.html By the way, the 1st edition has some extra information that's unfortunately not part of the 2nd one. So you can try to get that one too. Best, Navdeep --- On Thu, Mar 27, 2014 at 12:35:38PM +, Dean Derbyshire wrote: > I'm after suggestions as to where the best place(s) for obtaining info on > latest equipment - advances in techniques etc. Oh, for protein > crystallisation and screening ahead of data collection! > > cheers > > Dean --- Navdeep Sidhu University of Goettingen ---
[ccp4bb] AW: [ccp4bb] Merging Data from Multiple Crystals
Hi Jarrod, I think these 5 helices are either slightly misplaced, or somewhat disordered. How does the main-chain density look like? Do you see a discrete main-chain, or is the main-chain blurred and does the helix look like a blurred cylinder? If the main-chain is clear, I would take off all side chains, run some refinement and look if you could recognize some side chains. They may have shifted a few residues from what you think they are based on the homology model. Another option is to take out the 5 helices and rerun MR with them, using the 7 good helices as a partial model. You could also take one helix out at a time and try to build them again from scratch. Finally, if these helices are somewhat disordered, nothing can be done except from trying to grow different crystals, e.g. by adding a (different) ligand. With 7 out of 12 helices well-defined, your structure will nevertheless be interesting. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jarrod Mousa Gesendet: Donnerstag, 27. März 2014 15:15 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Merging Data from Multiple Crystals Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
Re: [ccp4bb] difference between polar angle and eulerian angle
According to the html-side the 'visualisation' includes two back-rotations in addition to what you copied here, so there is at least one difference to the visualisation of the Eulerian angles. Right- it says: "This can also be visualised as rotation ϕ about Z, rotation ω about the new Y, rotation κ about the new Z, rotation (-ω) about the new Y, rotation (-ϕ) about the new Z." The first two and the last two rotations can be seen as a "wrapper" which first transforms the coordinates so the rotation axis lies along z, then after the actual kappa rotation is carried out (by rotation about z), transforms the rotated molecule back to the otherwise original position. Or which transforms the coordinate system to put Z along the rotation axis, then after the rotation by kappa about z transforms back to the original coordinate system. Specifically, rotation ϕ about Z brings the axis into the x-z plane so that rotation ω about the Y brings the axis onto the z axis, so that rotation κ about Z is doing the desired rotation about a line that passes through the atoms in the same way the desired lmn axis did in the original orientation; Then the 4'th and 5'th operations are the inverse of the 2nd and first, bringing the rotated molecule back to its otherwise original position I think all the emphasis on "new" y and "new" z is confusing. If we are rotating the molecule (coordinates), then the axes don't change. They pass through the molecule in a different way because the molecule is rotated, but the axes are the same. After the first two rotations the Z axis passes along the desired rotation axis, but the Z axis has not moved, the coordinates (molecules) have. Of course there is the alternate interpretation that we are doing a change of coordinates and expressing the unmoved molecular coordinates relative to new principle axes. but if we are rotating the coordinates about the axes then the axes should remain the same, shouldn't they? Or maybe there is yet another way of looking at it. Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, maybe the confusion is due to that your quote seems incomplete. According to the html-side the 'visualisation' includes two back-rotations in addition to what you copied here, so there is at least one difference to the visualisation of the Eulerian angles. Best, Tim On 03/27/2014 07:11 AM, Qixu Cai wrote: Dear all, From the definition of CCP4 (http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle (ϕ, ω, κ) can be visualised as rotation ϕ about Z, rotation ω about the new Y, rotation κ about the new Z. It seems the same as the ZXZ convention of eulerian angle definition. What's the difference between the CCP4 polar angle definition and eulerian angle ZXZ definition? And what's the definition of polar angle XYK convention in GLRF program? Thank you very much! Best wishes, - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTNAz0UxlJ7aRr7hoRAj7IAKDs/J0L/XCYPpQSyB2BPJ2uWV2lVgCeKD72 0DemwU57v6fekF6iOC4/5IA= =PeT9 -END PGP SIGNATURE-
[ccp4bb] question on charge charge interactions
Hello All, I am appealing to the community as I don't seem to be able to find through Google what I am looking for, and I just don't have the ability to look through every structure in the PDB to find this. I have what I think is an interesting case: a two domain protein structure with a mostly hydrophobic interface between the two domains- the kicker is that I have two charged residues buried in this domain and they are identical. That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) where these residues are less than 4 Angstroms apart. So I was wondering if anyone had seen this in any other structure(s)? The really interesting bit is that this interaction actually regulates the activity of the enzyme domain although the domain interface isn't that close to the catalytic site. Thanks in advance to all those who can find a reference to this kind of interaction. Cheers, tom
Re: [ccp4bb] question on charge charge interactions
Hi Tom, For acidic side-chains, these kind of interactions are described by Maria Flocco and Sherry Mowbray in: "Strange bedfellows: interactions between acidic side-chains in proteins." J. Mol. Biol. (1995) 254, 96-105. Best regards, Martin On Mar 28, 2014, at 12:11 AM, Tom Peat wrote: > Hello All, > > I am appealing to the community as I don't seem to be able to find through > Google what I am looking for, and I just don't have the ability to look > through every structure in the PDB to find this. > I have what I think is an interesting case: a two domain protein structure > with a mostly hydrophobic interface between the two domains- the kicker is > that I have two charged residues buried in this domain and they are > identical. > That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) > where these residues are less than 4 Angstroms apart. So I was wondering if > anyone had seen this in any other structure(s)? > The really interesting bit is that this interaction actually regulates the > activity of the enzyme domain although the domain interface isn't that close > to the catalytic site. > > Thanks in advance to all those who can find a reference to this kind of > interaction. > Cheers, tom
Re: [ccp4bb] question on charge charge interactions
Two Arg side chains stack next to each other in ferritin and in GST (see, for example, Arg-59 and its symmetry mate in 3F33). I expect there are other examples, but these two come readily to mind. Cheers, Pat On 27 Mar 2014, at 7:11 PM, Tom Peat wrote: > Hello All, > > I am appealing to the community as I don't seem to be able to find through > Google what I am looking for, and I just don't have the ability to look > through every structure in the PDB to find this. > I have what I think is an interesting case: a two domain protein structure > with a mostly hydrophobic interface between the two domains- the kicker is > that I have two charged residues buried in this domain and they are > identical. > That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) > where these residues are less than 4 Angstroms apart. So I was wondering if > anyone had seen this in any other structure(s)? > The really interesting bit is that this interaction actually regulates the > activity of the enzyme domain although the domain interface isn't that close > to the catalytic site. > > Thanks in advance to all those who can find a reference to this kind of > interaction. > Cheers, tom --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com pl...@drexelmed.edu
Re: [ccp4bb] question on charge charge interactions
Tom, I would think the case can be made for sharing a proton (one ionised and one not) in either case but more so for acidic residues. See HIV protease Asp-Asp as a well-established example Hope this helps J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Friday, 28 March 2014 12:12 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] question on charge charge interactions Hello All, I am appealing to the community as I don't seem to be able to find through Google what I am looking for, and I just don't have the ability to look through every structure in the PDB to find this. I have what I think is an interesting case: a two domain protein structure with a mostly hydrophobic interface between the two domains- the kicker is that I have two charged residues buried in this domain and they are identical. That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) where these residues are less than 4 Angstroms apart. So I was wondering if anyone had seen this in any other structure(s)? The really interesting bit is that this interaction actually regulates the activity of the enzyme domain although the domain interface isn't that close to the catalytic site. Thanks in advance to all those who can find a reference to this kind of interaction. Cheers, tom
Re: [ccp4bb] question on charge charge interactions
Hello Joel, I like the example of HIV protease, but in this case these Asp residues are found in the active site of the protein, and unless there is substrate (or inhibitor) in the active site, these would be solvent exposed (unless I'm looking at the wrong pair of Asp residues). In the particular case I'm looking at, I have a buried pair with no other charged residues around- no waters/ metals, just Phe, Leu, etc. Which is why I think it might be slightly more rare than most of the examples I've heard about so far. Thanks for the help. Cheers, tom -Original Message- From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz] Sent: Friday, 28 March 2014 12:02 PM To: Peat, Tom (CMSE, Parkville); CCP4BB@JISCMAIL.AC.UK Subject: RE: question on charge charge interactions Tom, I would think the case can be made for sharing a proton (one ionised and one not) in either case but more so for acidic residues. See HIV protease Asp-Asp as a well-established example Hope this helps J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Friday, 28 March 2014 12:12 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] question on charge charge interactions Hello All, I am appealing to the community as I don't seem to be able to find through Google what I am looking for, and I just don't have the ability to look through every structure in the PDB to find this. I have what I think is an interesting case: a two domain protein structure with a mostly hydrophobic interface between the two domains- the kicker is that I have two charged residues buried in this domain and they are identical. That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) where these residues are less than 4 Angstroms apart. So I was wondering if anyone had seen this in any other structure(s)? The really interesting bit is that this interaction actually regulates the activity of the enzyme domain although the domain interface isn't that close to the catalytic site. Thanks in advance to all those who can find a reference to this kind of interaction. Cheers, tom
Re: [ccp4bb] question on charge charge interactions
Tom, How about Magalhaes et al., J. Protein Chem., Vol. 13, p 195? Chad From: Tom Peat To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, March 27, 2014 8:09 PM Subject: Re: [ccp4bb] question on charge charge interactions Hello Joel, I like the example of HIV protease, but in this case these Asp residues are found in the active site of the protein, and unless there is substrate (or inhibitor) in the active site, these would be solvent exposed (unless I'm looking at the wrong pair of Asp residues). In the particular case I'm looking at, I have a buried pair with no other charged residues around- no waters/ metals, just Phe, Leu, etc. Which is why I think it might be slightly more rare than most of the examples I've heard about so far. Thanks for the help. Cheers, tom -Original Message- From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz] Sent: Friday, 28 March 2014 12:02 PM To: Peat, Tom (CMSE, Parkville); CCP4BB@JISCMAIL.AC.UK Subject: RE: question on charge charge interactions Tom, I would think the case can be made for sharing a proton (one ionised and one not) in either case but more so for acidic residues. See HIV protease Asp-Asp as a well-established example Hope this helps J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Friday, 28 March 2014 12:12 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] question on charge charge interactions Hello All, I am appealing to the community as I don't seem to be able to find through Google what I am looking for, and I just don't have the ability to look through every structure in the PDB to find this. I have what I think is an interesting case: a two domain protein structure with a mostly hydrophobic interface between the two domains- the kicker is that I have two charged residues buried in this domain and they are identical. That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) where these residues are less than 4 Angstroms apart. So I was wondering if anyone had seen this in any other structure(s)? The really interesting bit is that this interaction actually regulates the activity of the enzyme domain although the domain interface isn't that close to the catalytic site. Thanks in advance to all those who can find a reference to this kind of interaction. Cheers, tom
